Federal agents trapped and killed a mountain lion called M56 in April after it raided a farm near the East County community of Japatul — a common fate that might have escaped greater attention were it not for the GPS collar that tracked his improbable journey.

Unlike any Southern California big cat in the past decade, he provided researchers with rare insight into the powerful and largely mysterious species that prowls suburban and rural lands.

The maturing lion plodded more than 100 miles during two months, getting lean and strong as he learned the landscape. He navigated past highways, nosed around the Wild Animal Park near Escondido, visited beaches at Camp Pendleton and probably used a wildlife crossing in Valley Center designed for creatures on the move.

Perhaps the most important discovery yielded by M56 is that despite extensive development, mountain lions still can roam between the Santa Ana Mountains of southern Orange County and the ranges of eastern San Diego County. M56 also offers clues about where to concentrate conservation efforts, along with a reminder that cats venturing into the urban edge have a higher risk of death than those who steer clear of humans.

“We didn’t even have any idea that a mountain lion could travel that far in this fragmented landscape so quickly,” said Trish Smith, a senior ecologist for The Nature Conservancy in San Diego. “He demonstrated that mountain lions can make a crossing of Interstate 15 and make it into the Palomar Mountains and even to the (U.S.-Mexico) border.”

For Smith and other animal experts, the movement of these lions — also known as mountain cats, catamounts, panthers, pumas and cougars — between the Santa Ana and Laguna mountains is important in maintaining the genetic diversity of the species.

“If we just focused on what has been lost, we might give up,” Smith said. “To know mountain lions are there and to know that we still have a certain bit of wildness in our open-space lands provides me (with) a sense that Southern California still maintains a high level of biological diversity.”

The mountain-lion tracking project was started in 2000 by the Wildlife Health Center at the University of California Davis. It first focused on evaluating the impact of lions on federally protected bighorn sheep in Riverside and San Diego counties. Over time, it has expanded to assess human-lion interactions, patterns of movement and other elements.

Veterinarian Winston Vickers and his colleagues in the UC Davis program have collared 53 lions in 10 years. Twenty-five are known to be dead from a variety of causes, including disease, collisions with cars, shootings by hunters without a permit and state-approved killings to remove animals deemed to be a nuisance.

The research is slow, partly because scientists need special GPS collars and aerial surveys to track big cats. The creatures typically travel alone at night through river valleys and across hillsides in search of deer and a home range that’s not already claimed by a dominant lion.

“They are very efficient predators that have survived over a very long period of time,” said Barry Martin, a veteran animal tracker in San Diego County. “One of the reasons they have been successful is they have learned how to be discreet. … It’s pretty amazing how close they get to that urban edge without any problems — as long as they have enough to eat.”

There are roughly 5,000 mountain lions living across 50 million acres of suitable habitat in California’s foothills and mountains, according to the state Department of Fish and Game. In 1990, state Proposition 117 made them a “specially protected species” and barred hunting them.

Since then, wildlife officials have verified a handful of mountain-lion attacks on people, including a fatal encounter at Cuyamaca Rancho State Park in 1994. Confirmed run-ins with the species peaked two years later; they have remained relatively stable in recent years.

Vickers said there are no current population statistics for mountain lions in Southern California or San Diego County. His research suggests that about 20 adult lions live in the Santa Ana Mountains, which are almost entirely separated from other habitat areas by freeways and homes.

That’s where the short life of M56 started, probably near Caspers Wilderness Park in Orange County. Researchers captured him there when he was 4 or 5 months old in December 2008, along with his mother and a sister. He stayed close to his family until March, when he split in search of his own territory, a typical strategy for a lion of 18 to 20 months.

With at least three adult males already circulating in the area, M56 headed south into the relatively undeveloped lands of Camp Pendleton. Some of his first stops were along the coast.

“Being a true Southern Californian, he went to the beach a couple of times on his ramble,” Vickers said. “We have seen that before in dispersing young lions that have just followed drainages till they empty into the ocean. … Camp Pendleton is about the only place where that is possible in Southern California anymore.”

M56 then headed south until he ran into state Route 76 and followed it to Bonsall, where he became the first tracked cougar to get past Interstate 15. Using GPS data, Vickers retraced M56’s steps to Gopher Canyon Road, where he suspects the cat used an under-crossing to avoid highway traffic.

The animal eventually turned south again and skirted the rural fringe of Escondido. He kept moving south and east across Interstate 8 until he closed in on the U.S.-Mexico border zone, with its fences and patrol vehicles.

“It’s been rather common for the mountain lions to get to the border and then turn around,” Vickers said. Only one lion collared by the UC Davis team has crossed the international boundary.

Instead of crossing into Mexico, M56 angled northwest across the Cleveland National Forest until he found a farm that proved too good to pass up. Vickers said it was home to to six or eight sheep that “were not penned or protected in any way,” and at least one sheep was killed.

He and others say that rural residents should try to protect their animals and avoid having to destroy the lions.

Problem lions, Martin said, “tend to be the ones who are just dispersing and are young — maybe not quite competent — and looking for targets of opportunity.”

Vickers said state officials are obligated to issue a depredation permit if a mountain lion has killed a domestic animal and its owner requests the cat to be put down. U.S. Department of Agriculture typically handles these incidents, as it did in the case of M56.

California’s human population is growing, but lion problems appear to be declining. In 2009, state wildlife officials issued 93 depredation permits for mountain lions, leading to 42 being killed. Both numbers were the lowest in more than two decades, suggesting to Vickers that some people who live in the backcountry are becoming more tolerant of big cats and are taking more precautions to safeguard domestic animals.

Vickers and Smith at The Nature Conservancy are likely to continue referencing M56’s journey for years as they search for clues about how people and lions might co-exist in Southern California.